make clippy fully happy

libradicl/src/collate.rs

@@ -91,14 +91,13 @@ fn get_orientation(mdata: &serde_json::Value, log: &slog::Logger) -> Strand {
         .chars()
         .next()
         .unwrap();
-    let expected_ori = match Strand::from_char(&ori_str) {
+    match Strand::from_char(&ori_str) {
         Ok(s) => s,
         Err(e) => {
             crit!(log, "invalid metadata {}.", e);
             std::process::exit(1);
         }
-    };
-    expected_ori
+    }
 }
 
 pub fn collate_in_memory_multipass(

libradicl/src/pugutils.rs

@@ -301,7 +301,11 @@ pub(super) fn get_num_molecules_trivial_discard_all_ambig(
 ) -> (Vec<f32>, f64) {
     let mut counts = vec![0.0f32; num_genes];
     let s = RandomState::<Hash64>::new();
-    let mut gene_map = HashMap::with_hasher(s);
+    let mut gene_map: std::collections::HashMap<
+        u32,
+        Vec<u64>,
+        fasthash::RandomState<fasthash::sea::Hash64>,
+    > = HashMap::with_hasher(s);
 
     let mut total_umis = 0u64;
     let mut multi_gene_umis = 0u64;
@@ -334,7 +338,7 @@ pub(super) fn get_num_molecules_trivial_discard_all_ambig(
         if !multi_gene {
             gene_map
                 .entry(prev_gene_id)
-                .or_insert_with(|| Vec::new())
+                .or_default()
                 .extend(umis.iter().map(|x| x.0));
         }
     }
@@ -362,7 +366,7 @@ fn get_num_molecules_large_component(
     vertex_ids: &[u32],
     tid_to_gid: &[u32],
     num_genes: usize,
-    log: &slog::Logger,
+    _log: &slog::Logger,
 ) -> Vec<u32> {
     let mut counts = vec![0u32; num_genes];
 
@@ -551,7 +555,6 @@ pub(super) fn get_num_molecules(
     // the transcripts to their corresponding gene ids.
     //let mut global_txps : Vec<u32>;
     let mut global_txps = get_set(16);
-    let mut alternative_resoluton = false;
     let mut pug_stats = PUGResolutionStatistics {
         used_alternative_strategy: false,
         total_mccs: 0u64,
@@ -590,7 +593,6 @@ pub(super) fn get_num_molecules(
                     ng
                 );
                 pug_stats.used_alternative_strategy = true;
-                alternative_resoluton = true;
                 continue;
             }
 

libradicl/src/quant.rs

@@ -41,7 +41,7 @@ use flate2::Compression;
 
 use self::libradicl::em::{em_optimize, run_bootstrap};
 use self::libradicl::pugutils;
-use self::libradicl::schema::{EqMap, PUGEdgeType, PUGResolutionStatistics, ResolutionStrategy};
+use self::libradicl::schema::{EqMap, PUGEdgeType, ResolutionStrategy};
 use self::libradicl::utils::*;
 
 /// Extracts the parsimonious UMI graphs (PUGs) from the
@@ -278,29 +278,29 @@ impl BootstrapHelper {
                     fs::File::create(bootstrap_var_path).unwrap(),
                     Compression::default(),
                 );
-                return BootstrapHelper {
+                BootstrapHelper {
                     bsfile: None,
                     mean_var_files: Some((
                         BufWriter::new(bt_mean_buffered),
                         BufWriter::new(bt_var_buffered),
                     )),
-                };
+                }
             } else {
                 let bootstrap_path = output_path.join("bootstraps.eds.gz");
                 let bt_buffered = GzEncoder::new(
                     fs::File::create(bootstrap_path).unwrap(),
                     Compression::default(),
                 );
-                return BootstrapHelper {
+                BootstrapHelper {
                     bsfile: Some(BufWriter::new(bt_buffered)),
                     mean_var_files: None,
-                };
+                }
             }
         } else {
-            return BootstrapHelper {
+            BootstrapHelper {
                 bsfile: None,
                 mean_var_files: None,
-            };
+            }
         }
     }
 }
@@ -314,6 +314,9 @@ struct QuantOutputInfo {
     bootstrap_helper: BootstrapHelper, //sample_or_mean_and_var: (BufWriter<GzEncoder<fs::File>>)
 }
 
+// TODO: see if we'd rather pass an structure
+// with these options
+#[allow(clippy::too_many_arguments)]
 pub fn quantify(
     input_dir: String,
     tg_map: String,
@@ -497,7 +500,7 @@ pub fn quantify(
         barcode_file: BufWriter::new(bc_file),
         eds_file: BufWriter::new(buffered),
         feature_file: BufWriter::new(ff_file),
-        trimat: trimat,
+        trimat,
         row_index: 0usize,
         bootstrap_helper: boot_helper,
     }));
@@ -802,12 +805,10 @@ pub fn quantify(
                                     varf.write_all(&eds_var_bytes)
                                         .expect("can't write to bootstrap var file.");
                                 }
-                            } else {
-                                if let Some(bsfile) = &mut writer.bootstrap_helper.bsfile {
-                                    bsfile
-                                        .write_all(&bt_eds_bytes)
-                                        .expect("can't write to bootstrap file");
-                                }
+                            } else if let Some(bsfile) = &mut writer.bootstrap_helper.bsfile {
+                                bsfile
+                                    .write_all(&bt_eds_bytes)
+                                    .expect("can't write to bootstrap file");
                             }
                         } // done bootstrap writing
                     }

src/main.rs

@@ -17,6 +17,7 @@ use libradicl::schema::ResolutionStrategy;
 use mimalloc::MiMalloc;
 use rand::Rng;
 use slog::{crit, o, warn, Drain};
+use std::unimplemented;
 
 #[global_allocator]
 static GLOBAL: MiMalloc = MiMalloc;
@@ -44,6 +45,13 @@ fn main() {
     // [] add command for just counting barcode frequency
     // [] add other algorithms for determining barcode cutoff
 
+    let convert_app = App::new("convert")
+        .about("Convert a BAM file to a RAD file")
+        .version(version)
+        .author(crate_authors)
+        .arg(Arg::from("-b, --bam=<bam-file> 'input SAM/BAM file'"))
+        .arg(Arg::from("-o, --output=<rad-file> 'output RAD file'"));
+
     let gen_app = App::new("generate-permit-list")
         .about("Generate a permit list of barcodes from a RAD file")
         .version(version)
@@ -109,6 +117,7 @@ fn main() {
         .subcommand(gen_app)
         .subcommand(collate_app)
         .subcommand(quant_app)
+        .subcommand(convert_app)
         .get_matches();
 
     let decorator = slog_term::TermDecorator::new().build();
@@ -199,6 +208,12 @@ fn main() {
         }
     }
 
+    if let Some(ref t) = opts.subcommand_matches("convert") {
+        let _input_file: String = t.value_of_t("bam-file").unwrap();
+        let _rad_file: String = t.value_of_t("rad-file").unwrap();
+        unimplemented!("convert command is not yet implemented.")
+    }
+
     if let Some(ref t) = opts.subcommand_matches("collate") {
         let input_dir: String = t.value_of_t("input-dir").unwrap();
         let rad_file: String = t.value_of_t("rad-file").unwrap();